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gmx-densorder(1) | GROMACS Manual | gmx-densorder(1) |
NAME¶
gmx-densorder - Calculate surface fluctuationsSYNOPSIS¶
gmx densorder [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]][-n [<.ndx>]] [-o [<.dat>]] [-or [<.out> [...]]]
[-og [<.xpm> [...]]] [-Spect [<.out> [...]]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-[no]1d] [-bw <real>] [-bwn <real>]
[-order <int>] [-axis <string>] [-method <enum>]
[-d1 <real>] [-d2 <real>] [-tblock <int>]
[-nlevel <int>]
DESCRIPTION¶
gmx densorder reduces a two-phase density distribution along an axis, computed over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a functional profile for interfacial densities. A time-averaged spatial representation of the interfaces can be output with the option -tavg.OPTIONS¶
Options to specify input and output files: -s [<.tpr/.tpb/...>] (topol.tpr) (Input)Run input file: tpr tpb tpa -f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng -n [<.ndx>] (index.ndx) (Input)
Index file -o [<.dat>] (Density4D.dat) (Output, Optional)
Generic data file -or [<.out> [...]] (hello.out) (Output, Optional)
Generic output file -og [<.xpm> [...]] (interface.xpm) (Output, Optional)
X PixMap compatible matrix file -Spect [<.out> [...]] (intfspect.out) (Output, Optional)
Generic output file Other options: -nice <int> (0)
Set the nicelevel -b <time> (0)
First frame (ps) to read from trajectory -e <time> (0)
Last frame (ps) to read from trajectory -dt <time> (0)
Only use frame when t MOD dt = first time (ps) -[no]w (no)
View output .xvg, .xpm, .eps and .pdb files -[no]1d (no)
Pseudo-1d interface geometry -bw <real> (0.2)
Binwidth of density distribution tangential to interface -bwn <real> (0.05)
Binwidth of density distribution normal to interface -order <int> (0)
Order of Gaussian filter, order 0 equates to NO filtering -axis <string> (Z)
Axis Direction - X, Y or Z -method <enum> (bisect)
Interface location method: bisect, functional -d1 <real> (0)
Bulk density phase 1 (at small z) -d2 <real> (1000)
Bulk density phase 2 (at large z) -tblock <int> (100)
Number of frames in one time-block average -nlevel <int> (100)
Number of Height levels in 2D - XPixMaps
SEE ALSO¶
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.VERSION 5.0.2 |